[English] 日本語
Yorodumi
- EMDB-23690: E1435Q Ycf1 mutant in inward-facing narrow conformation -

+
Open data


ID or keywords:

Loading...

-
Basic information

Entry
Database: EMDB / ID: EMD-23690
TitleE1435Q Ycf1 mutant in inward-facing narrow conformation
Map dataSharpened refine map constructed on unsharpened map using provided mask by Sharpen 3D - cisTEM.
Sample
  • Complex: Ycf1 monomer
    • Protein or peptide: Metal resistance protein YCF1
KeywordsABC transporter / MEMBRANE PROTEIN
Function / homology
Function and homology information


ABC-type Cd2+ transporter / ABC-type cadmium transporter activity / Recycling of bile acids and salts / Heme degradation / Aspirin ADME / Atorvastatin ADME / Paracetamol ADME / P-type cadmium transporter activity / bilirubin transmembrane transporter activity / bilirubin transport ...ABC-type Cd2+ transporter / ABC-type cadmium transporter activity / Recycling of bile acids and salts / Heme degradation / Aspirin ADME / Atorvastatin ADME / Paracetamol ADME / P-type cadmium transporter activity / bilirubin transmembrane transporter activity / bilirubin transport / vacuole fusion, non-autophagic / ABC-family proteins mediated transport / ABC-type glutathione-S-conjugate transporter / ABC-type glutathione S-conjugate transporter activity / fungal-type vacuole / fungal-type vacuole membrane / response to metal ion / ATPase-coupled transmembrane transporter activity / response to cadmium ion / glutathione metabolic process / cell redox homeostasis / transmembrane transport / membrane raft / ATP hydrolysis activity / ATP binding / membrane
Similarity search - Function
: / ABC transporter TMD0 domain / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter ...: / ABC transporter TMD0 domain / : / ABC transporter transmembrane region / ABC transporter type 1, transmembrane domain / ABC transporter integral membrane type-1 fused domain profile. / ABC transporter type 1, transmembrane domain superfamily / ABC transporter-like, conserved site / ABC transporters family signature. / ABC transporter / ABC transporter-like, ATP-binding domain / ATP-binding cassette, ABC transporter-type domain profile. / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Metal resistance protein YCF1
Similarity search - Component
Biological speciesSaccharomyces cerevisiae S288C (yeast)
Methodsingle particle reconstruction / cryo EM / Resolution: 4.04 Å
AuthorsKhandelwal NK / Millan CR
Funding support United States, 1 items
OrganizationGrant numberCountry
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)R00GM114245 United States
CitationJournal: Nat Commun / Year: 2022
Title: The structural basis for regulation of the glutathione transporter Ycf1 by regulatory domain phosphorylation.
Authors: Nitesh Kumar Khandelwal / Cinthia R Millan / Samantha I Zangari / Samantha Avila / Dewight Williams / Tarjani M Thaker / Thomas M Tomasiak /
Abstract: Yeast Cadmium Factor 1 (Ycf1) sequesters heavy metals and glutathione into the vacuole to counter cell stress. Ycf1 belongs to the ATP binding cassette C-subfamily (ABCC) of transporters, many of ...Yeast Cadmium Factor 1 (Ycf1) sequesters heavy metals and glutathione into the vacuole to counter cell stress. Ycf1 belongs to the ATP binding cassette C-subfamily (ABCC) of transporters, many of which are regulated by phosphorylation on intrinsically-disordered domains. The regulatory mechanism of phosphorylation is still poorly understood. Here, we report two cryo-EM structures of Ycf1 at 3.4 Å and 4.0 Å resolution in inward-facing open conformations that capture previously unobserved ordered states of the intrinsically disordered regulatory domain (R-domain). R-domain phosphorylation is clearly evident and induces a topology promoting electrostatic and hydrophobic interactions with Nucleotide Binding Domain 1 (NBD1) and the Lasso motif. These interactions stay constant between the structures and are related by rigid body movements of the NBD1/R-domain complex. Biochemical data further show R-domain phosphorylation reorganizes the Ycf1 architecture and is required for maximal ATPase activity. Together, we provide insights into how R-domains control ABCC transporter activity.
History
DepositionMar 25, 2021-
Header (metadata) releaseApr 6, 2022-
Map releaseApr 6, 2022-
UpdateOct 16, 2024-
Current statusOct 16, 2024Processing site: RCSB / Status: Released

-
Structure visualization

Supplemental images

emd_23690.png

Downloads & links

-
Map

FileDownload / File: emd_23690.map.gz / Format: CCP4 / Size: 103 MB / Type: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
AnnotationSharpened refine map constructed on unsharpened map using provided mask by Sharpen 3D - cisTEM.
Projections & slices

Image control

Size
Brightness
Contrast
Others
AxesZ (Sec.)Y (Row.)X (Col.)
1.03 Å/pix.
x 300 pix.
= 309.3 Å		1.03 Å/pix.
x 300 pix.
= 309.3 Å		1.03 Å/pix.
x 300 pix.
= 309.3 Å

Surface

Projections

Slices (1/3)

Slices (1/2)

Slices (2/3)

Images are generated by Spider.

Voxel sizeX=Y=Z: 1.031 Å
Density

Histogram

Histogram (log scale)
Contour LevelBy AUTHOR: 4.0
Minimum - Maximum-12.044328 - 15.256595000000001
Average (Standard dev.)-0.0010910778 (±0.9073835)
SymmetrySpace group: 1
Details

EMDB XML:

Map geometry
Axis orderXYZ
Origin000
Dimensions300300300
Spacing300300300
CellA=B=C: 309.30002 Å
α=β=γ: 90.0 °

-
Supplemental data

-
Mask #1

Fileemd_23690_msk_1.map
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Additional map: Unsharpened map obtained from Manual Refine - cisTEM.

Fileemd_23690_additional_1.map
AnnotationUnsharpened map obtained from Manual Refine - cisTEM.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: The second half-map from unsharpened refine map generated...

Fileemd_23690_half_map_1.map
AnnotationThe second half-map from unsharpened refine map generated in Generate 3D - cisTEM.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Half map: The first half-map from unsharpened refine map generated...

Fileemd_23690_half_map_2.map
AnnotationThe first half-map from unsharpened refine map generated in Generate 3D - cisTEM.
Projections & Slices
AxesZYX

Projections

Slices (1/2)
Density Histograms

Histogram

Histogram (log scale)

-
Sample components

-
Entire : Ycf1 monomer

EntireName: Ycf1 monomer
Components
  • Complex: Ycf1 monomer
    • Protein or peptide: Metal resistance protein YCF1

-
Supramolecule #1: Ycf1 monomer

SupramoleculeName: Ycf1 monomer / type: complex / ID: 1 / Parent: 0 / Macromolecule list: all
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast)
Molecular weightTheoretical: 176.66831 KDa

-
Macromolecule #1: Metal resistance protein YCF1

MacromoleculeName: Metal resistance protein YCF1 / type: protein_or_peptide / ID: 1
Details: Phosphorylated residues (S908, T911 and S914) are present in structure file.
Number of copies: 1 / Enantiomer: LEVO / EC number: ABC-type Cd2+ transporter
Source (natural)Organism: Saccharomyces cerevisiae S288C (yeast) / Strain: ATCC 204508 / S288c
Molecular weightTheoretical: 176.318328 KDa
Recombinant expressionOrganism: Saccharomyces cerevisiae (brewer's yeast)
SequenceString: ASDYKDDDDK GALEVLFQGP SSPMAGNLVS WACKLCRSPE GFGPISFYGD FTQCFIDGVI LNLSAIFMIT FGIRDLVNLC KKKHSGIKY RRNWIIVSRM ALVLLEIAFV SLASLNISKE EAENFTIVSQ YASTMLSLFV ALALHWIEYD RSVVANTVLL F YWLFETFG ...String:
ASDYKDDDDK GALEVLFQGP SSPMAGNLVS WACKLCRSPE GFGPISFYGD FTQCFIDGVI LNLSAIFMIT FGIRDLVNLC KKKHSGIKY RRNWIIVSRM ALVLLEIAFV SLASLNISKE EAENFTIVSQ YASTMLSLFV ALALHWIEYD RSVVANTVLL F YWLFETFG NFAKLINILI RHTYEGIWYS GQTGFILTLF QVITCASILL LEALPKKPLM PHQHIHQTLT RRKPNPYDSA NI FSRITFS WMSGLMKTGY EKYLVEADLY KLPRNFSSEE LSQKLEKNWE NELKQKSNPS LSWAICRTFG SKMLLAAFFK AIH DVLAFT QPQLLRILIK FVTDYNSERQ DDHSSLQGFE NNHPQKLPIV RGFLIAFAMF LVGFTQTSVL HQYFLNVFNT GMYI KSALT ALIYQKSLVL SNEASGLSST GDIVNLMSVD VQKLQDLTQW LNLIWSGPFQ IIICLYSLYK LLGNSMWVGV IILVI MMPL NSFLMRIQKK LQKSQMKYKD ERTRVISEIL NNIKSLKLYA WEKPYREKLE EVRNNKELKN LTKLGCYMAV TSFQFN IVP FLVSCCTFAV FVYTEDRALT TDLVFPALTL FNLLSFPLMI IPMVLNSFIE ASVSIGRLFT FFTNEELQPD SVQRLPK VK NIGDVAINIG DDATFLWQRK PEYKVALKNI NFQAKKGNLT CIVGKVGSGK TALLSCMLGD LFRVKGFATV HGSVAYVS Q VPWIMNGTVK ENILFGHRYD AEFYEKTIKA CALTIDLAIL MDGDKTLVGE KGISLSGGQK ARLSLARAVY ARADTYLLD DPLAAVDEHV ARHLIEHVLG PNGLLHTKTK VLATNKVSAL SIADSIALLD NGEITQQGTY DEITKDADSP LWKLLNNYGK KNNGKSNEF GDSSESSVRE SSIPVEGELE QLQKLNDLDF GNSDAISLRR A(SEP)DA(TPO)LG(SEP)ID FGDDENIAK REHREQGKVK WNIYLEYAKA CNPKSVCVFI LFIVISMFLS VMGNVWLKHW SEVNSRYGSN PNAARYLAIY FALGIGSALA TLIQTIVLW VFCTIHASKY LHNLMTNSVL RAPMTFFETT PIGRILNRFS NDIYKVDALL GRTFSQFFVN AVKVTFTITV I CATTWQFI FIIIPLSVFY IYYQQYYLRT SRELRRLDSI TRSPIYSHFQ ETLGGLATVR GYSQQKRFSH INQCRIDNNM SA FYPSINA NRWLAYRLEL IGSIIILGAA TLSVFRLKQG TLTAGMVGLS LSYALQITQT LNWIVRMTVE VETNIVSVER IKE YADLKS EAPLIVEGHR PPKEWPSQGD IKFNNYSTRY RPELDLVLKH INIHIKPNEK VGIVGRTGAG KSSLTLALFR MIEA SEGNI VIDNIAINEI GLYDLRHKLS IIPQDSQVFE GTVRENIDPI NQYTDEAIWR ALELSHLKEH VLSMSNDGLD AQLTE GGGN LSVGQRQLLC LARAMLVPSK ILVLDQATAA VDVETDKVVQ ETIRTAFKDR TILTIAHRLN TIMDSDRIIV LDNGKV AEF DSPGQLLSDN KSLFYSLCME AGLVNENGLV PRGSSAHHHH HHHHHHGA

UniProtKB: Metal resistance protein YCF1

-
Experimental details

-
Structure determination

Methodcryo EM
Processingsingle particle reconstruction
Aggregation stateparticle

-
Sample preparation

Concentration5.94 mg/mL
BufferpH: 7
Component:
ConcentrationFormulaName
300.0 mMNaClsodium chloride
50.0 mMTristris(hydroxymethyl)aminomethane

Details: Solution were made fresh in cold distilled water and final pH was adjusted to 7.0 with HCl of cold buffer. The digitonin detergent was added to final .06 % in buffer after pH adjustment.
GridModel: Quantifoil R1.2/1.3 / Material: GOLD / Mesh: 400 / Support film - Material: GOLD / Support film - topology: HOLEY / Pretreatment - Type: GLOW DISCHARGE / Pretreatment - Time: 30 sec. / Details: Pelco 15mA - 30s glow/30s hold charge
VitrificationCryogen name: ETHANE / Chamber humidity: 80 % / Chamber temperature: 283.15 K / Instrument: LEICA EM GP

-
Electron microscopy

MicroscopeTFS KRIOS
Image recordingFilm or detector model: GATAN K3 (6k x 4k) / Number grids imaged: 1 / Number real images: 8499 / Average exposure time: 2.9 sec. / Average electron dose: 54.0 e/Å2
Electron beamAcceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
Electron opticsC2 aperture diameter: 70.0 µm / Calibrated magnification: 22500 / Illumination mode: FLOOD BEAM / Imaging mode: BRIGHT FIELD / Cs: 2.7 mm / Nominal defocus max: 2.1 µm / Nominal defocus min: 0.9 µm
Sample stageCooling holder cryogen: NITROGEN
Experimental equipment
Model: Titan Krios / Image courtesy: FEI Company

+
Image processing

Particle selectionNumber selected: 2159582 / Details: Relion auto pick
Startup modelType of model: OTHER / Details: Ab-initio Model generated in Relion.
Final reconstructionApplied symmetry - Point group: C1 (asymmetric) / Resolution.type: BY AUTHOR / Resolution: 4.04 Å / Resolution method: FSC 0.143 CUT-OFF / Software - Name: cisTEM (ver. 1.0.0) / Number images used: 48716
Initial angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: RELION (ver. 3.1.1)
Final angle assignmentType: MAXIMUM LIKELIHOOD / Software - Name: cisTEM (ver. 1.0.0)
FSC plot (resolution estimation)

-
Atomic model buiding 1

Initial modelPDB ID:

6jb1


Chain - Chain ID: B / Chain - Source name: PDB / Chain - Initial model type: experimental model
Output model

PDB-7m68:
E1435Q Ycf1 mutant in inward-facing narrow conformation

+
About Yorodumi

-
News

-
Feb 9, 2022. New format data for meta-information of EMDB entries

New format data for meta-information of EMDB entries

  • Version 3 of the EMDB header file is now the official format.
  • The previous official version 1.9 will be removed from the archive.

Related info.:EMDB header

External links:wwPDB to switch to version 3 of the EMDB data model

-
Aug 12, 2020. Covid-19 info

Covid-19 info

URL: https://pdbj.org/emnavi/covid19.php

New page: Covid-19 featured information page in EM Navigator.

Related info.:Covid-19 info / Mar 5, 2020. Novel coronavirus structure data

+
Mar 5, 2020. Novel coronavirus structure data

Novel coronavirus structure data

Related info.:Yorodumi Speices / Aug 12, 2020. Covid-19 info

External links:COVID-19 featured content - PDBj / Molecule of the Month (242)：Coronavirus Proteases

+
Jan 31, 2019. EMDB accession codes are about to change! (news from PDBe EMDB page)

EMDB accession codes are about to change! (news from PDBe EMDB page)

  • The allocation of 4 digits for EMDB accession codes will soon come to an end. Whilst these codes will remain in use, new EMDB accession codes will include an additional digit and will expand incrementally as the available range of codes is exhausted. The current 4-digit format prefixed with “EMD-” (i.e. EMD-XXXX) will advance to a 5-digit format (i.e. EMD-XXXXX), and so on. It is currently estimated that the 4-digit codes will be depleted around Spring 2019, at which point the 5-digit format will come into force.
  • The EM Navigator/Yorodumi systems omit the EMD- prefix.

Related info.:Q: What is EMD? / ID/Accession-code notation in Yorodumi/EM Navigator

External links:EMDB Accession Codes are Changing Soon! / Contact to PDBj

+
Jul 12, 2017. Major update of PDB

Major update of PDB

  • wwPDB released updated PDB data conforming to the new PDBx/mmCIF dictionary.
  • This is a major update changing the version number from 4 to 5, and with Remediation, in which all the entries are updated.
  • In this update, many items about electron microscopy experimental information are reorganized (e.g. em_software).
  • Now, EM Navigator and Yorodumi are based on the updated data.

External links:wwPDB Remediation / Enriched Model Files Conforming to OneDep Data Standards Now Available in the PDB FTP Archive

-
Yorodumi

Thousand views of thousand structures

  • Yorodumi is a browser for structure data from EMDB, PDB, SASBDB, etc.
  • This page is also the successor to EM Navigator detail page, and also detail information page/front-end page for Omokage search.
  • The word "yorodu" (or yorozu) is an old Japanese word meaning "ten thousand". "mi" (miru) is to see.

Related info.:EMDB / PDB / SASBDB / Comparison of 3 databanks / Yorodumi Search / Aug 31, 2016. New EM Navigator & Yorodumi / Yorodumi Papers / Jmol/JSmol / Function and homology information / Changes in new EM Navigator and Yorodumi

Read more